Getting startedshort URL
Fiji's main window
After starting Fiji, you will see the main window:
On MacOSX, the menu bar will appear on the top of the screen (as with all MacOS applications).
In the menubar, you will find most of the functionality, such as loading/saving files, processing them, and plugins will be installed into the menus, too.
The menus have different purposes:
- File input/output, new files
- Selection/ROI handling
- Visualization, stack manipulation
- Image filters
- Plugins, Macros and Utilities
- Help & Links
The tool bar
The toolbar mostly contains selection tools: the rectangle, ellipse, polygon, freehand and straight line selection tool. By clicking on the icon, you activate the tool.
Some tools offer option dialogs which you can open by double clicking the icon. This example shows the option dialog of the Oval Tool:
If there is a small red arrow in the lower right corner of the tool icon, you can right-click (Ctrl+click on an Apple mouse) and select an alternative selection tool (e.g. a circular brush selection tool which shares the icon with the ellipse selection tool). Example:
The status bar
The status bar displays useful information at startup, and when running plugins. It also shows a progress bar on the right side for long-running processes:
A single mouse click on the status bar will show the information about ImageJ and Java version as well as about memory consumption:
Drag & Drop
You can drag files from your favorite file manager and drop them on the main window; Fiji will load the corresponding files.
Drag 'n Drop will also work for images displayed in your web browser, unless they are links to other web pages. You can try with this page: clicking on an image will open a page whose image you can Drag 'n Drop into Fiji's main window.
Whenever you open an image, be it via File>Open, Drag 'n Drop or File>Open Samples, Fiji will open an image window.
The window has the file name as title, and it display some useful information above the image: the real resolution (in this case in square centimeters), the pixel resolution, the image type and the memory required by the image.
If your image does not have meta-data about the real resolution, you can set the resolution explicitely with Image>Properties... or by following the tutorial on spatial calibration.
You can change the image type:
- 8-bit (intensity range 0..255)
- 16-bit (intensity range 0..65535)
- 32-bit (floating point numbers)
- 8-bit color (up to 256 colors encoded via a color lookup table)
- RGB color (3 colors encoded as 8-bit values)
There are two more options: RGB stack and HSV stack, which can turn a 2-dimensional color image into a stack consisting of 3 color channels (red, green & blue or hue, saturation & value, respectively).
Have a look at the list of tutorials on this Wiki.